The term phyto-oestrogen encompasses isoflavone compounds, such as genistein and daidzein, found predominantly in soya products and the lignans, such as matairesinol and secoisolariciresinol, found in many fruits, cereals and in flaxseed. There is evidence that they have potential health benefits in man particularly against hormone-dependent diseases such as breast and prostate cancers and osteoporosis. This has led to intense interest in their absorption and biotransformation in man. The metabolism of isoflavones and lignans in animals and man is complex and involves both mammalian and gut microbial processes. Isoflavones are present predominantly as glucosides in most commercially available soya products; there is evidence that they are not absorbed in this form and that their bioavailability requires initial hydrolysis of the sugar moiety by intestinal beta-glucosidases. After absorption, phyto-oestrogens are reconjugated predominantly to glucuronic acid and to a lesser degree to sulphuric acid. Only a small portion of the free aglycone has been detected in blood, demonstrating that the rate of conjugation is high. There is extensive further metabolism of isoflavones (to equol and O-desmethylangolensin) and lignans (to enterodiol and enterolactone) by gut bacteria. In human subjects, even those on controlled diets, there is large interindividual variation in the metabolism of isoflavones and lignans, particularly in the production of the gut bacterial metabolite equol (from daidzein). Factors influencing absorption and metabolism of phyto-oestrogens include diet and gut microflora.